2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
Ecological Function and Biodiversity Indicators in European Soils
EcoFINDERS
http://www.ecofinders.eu/
Meeting of Coordinators, Brussels,
22-23 October 2012
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
EU Soil Thematic Strategy Soils deliver many ecosystem services
Soil ecosystem services
Food & biomass production Habitat, gene pool
J. Moulin (CA 36) Infosol (INRA Orléans)
Physical & cultural
environment for mankind
C. Schvartz (ISAL)
Storing, filtering & transformation
Source of raw materials
J. Moulin (CA 36)
A. Richer de Forges (CA 45) Infosol (INRA Orléans)
A. Richer de Forges (CA 45)
Courtesy of Antonio Bispo, ADEME
Meeting of Coordinators, Brussels,
22-23 October 2012
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
F. Ip
polit
o
Living soils
- Fauna: 1-5 T/ha
- Fungi: 3.5 T/ha
- Bacteria: 1.5 T/ha
Huge quantity of organisms
20 µm 20 µm
10 µm 10 µm Photo
: L
. A
voscan &
A. V
iolle
t
Fantastic diversity …but so little explored…
- Until recently: only access to culturable microorganisms
- Methodological progresses
possibility to extract DNA from soils
104 – 106 bacterial genotypes / g sol
Meeting of Coordinators, Brussels,
22-23 October 2012
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
Soils and biodiversity are submitted to major threats
Source : D. Arrouays (INRA Orléans)
Biodiversity
Sou
rce
: J.
Sau
ter
(AR
AA
)
Contamination
Source : D. Arrouays (INRA Orléans)
Floods andlandslides
Source : D. Arrouays (INRA Orléans)
Salinisation
Source : D. Arrouays (INRA Orléans)
Compaction
Sou
rce
: D. A
rrou
ays
(IN
RA
Orl
éans
)
Sealing
Organic
matter
Sou
rce
: D. A
rrou
ays
(IN
RA
Orl
éans
)Erosion
Adapted
from D
. Arrouays
Erosion: 115 million hectares subject to water erosion, 42 million hectares to wind erosion.
Contamination: 3.5 million sites could be contaminated
Decrease of organic matter: About 45% of European soils have low organic matter content
Soil sealing: 1990-2000: 1,000 km² of soil/year , 2000-2006, the average loss increased by 3%
http://ec.europa.eu/environment/soil/
Meeting of Coordinators, Brussels,
22-23 October 2012
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
In 2010, EC considered that for establishing Soil Thematic strategy, further knowledge was required on:
soil biodiversity
functions and resulting ecosystem services supported by this diversity
This requires: the development of standardised methods for the characterisation of soil
biodiversity
the establishment of policy-relevant and cost-effective indicators for biological diversity
Finally, convincing policy makers of the relevance of such Strategy also
requires:
the assessment of the economic value of the ecosystem services provided.
ENV.2010.2.1.4.4 Increasing the understanding of the role of soil biodiversity in ecosystem functioning
EcoFINDERS
Meeting of Coordinators, Brussels,
22-23 October 2012
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
EcoFINDERS - Concepts
EcoFINDERS - Concepts
Environmental filters
Decipher relations between soil
biodiversity, activities, functions
and ecosystem services
Ecosystem services
Activities
Functions
Proteome & Metabolome
Biodiversity Expression of genetic potential
DNA RNA Proteins
Genome Transcriptome
Assess the impact of environmental conditions (soil types,
climatic zones, land use) on soil biodiversity and relations
biodiversity-activities
Integrate information on microbial, faunal and plant communities
Analyse their interactions in food web models and consequences for
community and ecosystem stability
Meeting of Coordinators, Brussels,
22-23 October 2012
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
Meeting of Coordinators, Brussels,
22-23 October 2012
Consortium
23 partners
10 European countries: D, DK, F, I,
IRL, NL, P, S, SK, SLO, UK
Non-European country: China
Bringing expertises in various :
disciplines: biodiversity,
ecological functions, trophic nets,
risk assessment, biological
indicators, environmental
economics
soil organisms: archaea,
bacteria, fungi, protozoa,
microarthropods, oligochatea
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
EcoFINDERS - Standard Operating Procedures
Standardization of sampling procedures
Where, when and how take samples,
number of replicates, sampling depth, use
of composite samples, ...
Plassart et al., in preparation
Optimisation of DNA extraction
Assessment of possible biases according to the
soil type
Optimisation to allow extraction of DNA of the
major types of organisms targeted
Microorganisms (archaea, bacteria, fungi)
Plassart et al. 2012. PLoS One
Fauna (protozoa, nematodes,....)
Identification of bioindicators Sensitive
Consistent – reliable
Cost-effective
Table Annual Reports.docx
Standardization of methods for
biodiversity characterization
Meeting of Coordinators, Brussels,
22-23 October 2012
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
EcoFINDERS – Transect
Aims at assessing: Range of variations according to soil types, to
climatic zones and to land uses
Range of variations of the identified bioindicators
according to soil types, climatic zones and land
uses
Definition of the ‘Normal Operating Range’
Strategy: Using data derived from the Joint Research
Council, 255 points sampled across Europe to derive indicative values for: Organic Carbon, Texture, pH
Overlaid onto the LUCAS – landcover survey and sites identified as either forest, grass or tillage.
Identification of 80 sites per land-use type across Europe to give a range of the above soil properties
Characterization of biodiversity across Europe
Meeting of Coordinators, Brussels,
22-23 October 2012
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
Tonnersjoheden: Nutrient cycling (N)
Carbon storage
Lusignan: Nutrient cycling (N),
Carbon storage,
Soil structure & water
regulation
Veluwe: Nutrient cycling,
Carbon storage,
Soil structure regulation,
Aboveground diversity
Lancaster: Nutrient cycle,
Carbon storage,
Soil structure regulation,
Above round diversity
Berchidda: Nutrient cycling (N),
Carbon storage,
Above ground diversity
EcoFINDERS - LTOs
Connecting soil biodiversity, functions and ecosystem services
Different land uses: grasslands, tillage, forests
For each LTO: three levels of intensification Meeting of Coordinators, Brussels,
22-23 October 2012
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
EcoFINDERS - LTOs
Microbial diversity varies according to the LTOs
Meeting of Coordinators, Brussels,
22-23 October 2012
Biodiversity
DNA
Genome
Activities
Functions
Ecosystem services
RNA Proteins
Transcriptome Proteome & Metabolome
Environmental filters
Bacteria FungiArchaea
Lusignan Berchidda Lancaster Veluwe * Tonnersjoheden
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
EcoFINDERS - LTOs
Meeting of Coordinators, Brussels,
22-23 October 2012
Biodiversity
DNA
Genome
Activities
Functions
Ecosystem services
RNA Proteins
Transcriptome Proteome & Metabolome
Environmental filters
Bacteria Archaea Fungi
Wooded land (Low intensity) Wooded pasture (Medium intensity) Intensive grassland (High intensity)
Within a given LTO, microbial diversity differ
according to the level of intensification
e.g. Berchidda, Sardinia, Italy
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
EcoFINDERS - LTOs
Within a given LTO, microbial diversity differ
according to the level of intensification Biodiversity
DNA
Genome
Activities
Functions
Ecosystem services
RNA Proteins
Transcriptome Proteome & Metabolome
Environmental filters
*
*
***
** *** **
Bacteria Archaea Fungi
Overall effect of land-use intensity
Meeting of Coordinators, Brussels,
22-23 October 2012
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
EcoFINDERS - LTOs
How these variations translate in soil functioning?
= = Black box Black box Black box
Mineralization D1 > D2 >D3
Mineralization SOM = f (Microbial diversity)
> >
D1
D2
D3
0
2
4
6
8
10
0 10 20 30 40 50 60
mg
C-C
O2
/ g s
oil
Time (days)
D1 D2 D3
Biodiversity
DNA
Genome
Activities
Functions
Ecosystem services
RNA Proteins
Transcriptome Proteome & Metabolome
SOM mineralization
Meeting of Coordinators, Brussels,
22-23 October 2012
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
EcoFINDERS - LTOs
How these variations translate in soil functioning? Biodiversity
DNA
Genome
Activities
Functions
Ecosystem services
RNA Proteins
Transcriptome Proteome & Metabolome
Water regulation
macro
pore
s (
mean n
um
be
r/m
2)
rotation rotation
with grass
permanent
grass
level of intensification + -
wate
r in
filtra
tion
rate
earthworm activity
Meeting of Coordinators, Brussels,
22-23 October 2012
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
Mesocosm experiments
Assessing hypotheses raised from LTOs studies
Meeting of Coordinators, Brussels,
22-23 October 2012
Biodiversity
DNA
Genome
Activities
Functions
Ecosystem services
RNA Proteins
Transcriptome Proteome & Metabolome
. Minimal diversity for a function to be expressed Relations between above and below ground biodiversity
- How plant communities affect the resistance and resilience of belowground communities to drought?
- Impact of plant-derived C into the soil and different soil biota, in connections with soil food web and associated processes.
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
Dissemination
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
Publications
Griffiths BS, Philippot L. 2012. Insights into the resistance and resilience of the
soil microbial community. FEMS Microbiol Rev. doi: 10.1111/j.1574-
6976.2012.00343.x.
Hallin S. et al. Loss in microbial diversity affects nitrogen-cycling in soil. ISME J.
Philippot L, Ritz K, Pandard P, Hallin S, Martin-Laurent F. 2012. Standardisation
of methods in soil microbiology: progress and challenges. FEMS Microbiol
Ecol. doi: 10.1111/j.1574-6941.2012.01436.x.
Plassart P., Terrat S., Thomson. B., Griffiths R. , Dequiedt S., Lelievre M.,
Regnier T., Nowakv., Bailey M., Lemanceau P., Bispo A., Chabbi A., Maron
P.-A., Mougel C., Ranjard L. 2012. Evaluation of the ISO standard 11063
DNA extraction procedure for assessing soil microbial abundance and
community structure. PLoS One 7: e44279.
Ranjard L. et al. Evaluation of the ISO standard 11063 DNA extraction procedure
for assessing soil microbial abundance and community structure.
.
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
Conclusions and challenges
Conclusions In contrast with the statement made by Beijerinck in1913, everything is not
everywhere, biodiversity is not randomly distributed
The same organisms are not found everywhere
Progresses in the knowledge of the environmental filters impacting soil biodiversity: soil physico-chemical, especially pH, and land use
Relevance of the ‘Normal Operating Range’ concept
Need of data bases for diagnostic of the soil biodiversity
Need of Standard Operating Procedures
Challenges: Moving from diagnosis to action Based on diagnosis, define strategies of mitigation and soil restoration
This requires
to further progress in our knowledge of the soil functioning as supported
by biodiversity
to combine expertises in soil physics, chemistry, ecology
Meeting of Coordinators, Brussels,
22-23 October 2012
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
Conclusions and challenges
Meeting of Coordinators, Brussels,
22-23 October 2012
Challenges: Moving from diagnosis to action to deal with possible trade-offs
Primary
producers
Diversity of soil
decomposers (bacteria/fungi)
Soil Organic
Matter (SOM)
CO2
Plants residues,
root exsudates
Carbon
storage
Carbon
release
Nutriments
(N, P, K, S,…)
Courtesy of Pierre-Alain Maron
2nd Annual Meeting
21–23 November 2012, Wageningen EcoFINDERS
Conclusions and challenges
Meeting of Coordinators, Brussels,
22-23 October 2012
Challenges: Moving from diagnosis to action to guarantee the soil multifunctionalities at different spatial and temporal
scales
to capitalise European and National means and information on a set of
Critical Zones Observatories and Long Term Observatories
to match with world global initiatives
Alte
rre B
ourg
ogne
